Heatmaps of gene exchange experiment

Credits

Analysis by Chrispin Chaguza
Experiments by Anna York
Sequencing by Jason Rosch and colleagues (St Jude’s)
Interactive plots by Dan Weinberger
Funding: Merck Investigator Studies Program

Summary

These plots represent pangenomes created based on the sequenced strains. The heatmaps indicate whether a particular strain has gained a gene (yellow) or lost a gene(dark blue) compared to the reference. The plots at the bottom show the genomic location of genes gained and lost, mapped to a TIGR4 reference

Serotype 9V background

Parent strain is Serotype 9V ID ABC010001831, obtained from the CDC

Serotype 15B/C background

Parent strain is 15B/C, a carriage isolate from Hungary, ID Pool_hung_H10 (H124)

Serotype 22F background

Parent strain is serotype 22F, ID: ABC010003966, obtained from the CDC (IPD isolate)

Genomic context of gain/loss based on mapping to TIGR4 genome

Set 1

8, 7F, 7C, 6C, 22F, 19A

Set 2: Parent strain is 15B/C, a carriage isolate from Hungary, ID Pool_hung_H10 (H124)

7F, 6C (2), 35B, 35F (2), 3, 22F, 16F, 15B/C, 11A have the cassette added around 1235484

Set 3: Parent strain is serotype 22F, ID: ABC010003966, obtained from the CDC (IPD isolate)

7F, 6C, 35B, 35F, 3, 22F,16F, 15B.C, 11A (this is the same set of serotypes seen for set 2…are these mislabeled cps genes? cps adjacent genes on these backgrounds? on set 1, some of the serotypes overlap, some do not.